VCF-42: Reduce memory consumption when a single position returns many samples#867
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This function joins a vector of strings using a given delimiter character while optionally omitting empty strings.
…sample headers SampleHeaders is a subclass of the TileDBVCFDataset class since it is intended to be instantiated and loaded exclusively by TileDBVCFDataset. Internally SampleHeaders uses MD5 checksums and maps to only load unique headers and to associate samples with these unique headers, respectively.
…r released This is to prevent memory leaks while making the lifetime of these managed pointers more obvious.
This allows the names of samples stored in a SampleHeaders instance to be efficiently iterated via a view of the keys of an internal map.
This allows the names of only samples that have headers loaded to be iterated efficiently, both in terms of run-time and memory consumption.
Specifically, the std::string(const char* s, size_t n) constructor on macOS seems to ignore the n parameter and overflows. This was mitigated by adding a terminating character to s and using the std::string(const char* s) constructor instead.
…ses Indexes references, rather than copies
jp-dark
approved these changes
Jan 15, 2026
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Previously the header for every sample returned for a single position was being loaded into memory. However, many headers are identical except for their sample line, meaning basically the same headers were being loaded multiple times per position.
To alleviate the issue, this PR computes the MD5 checksum for each header (minus the sample line) and only stores the unique ones. Samples are then associated with the correct header using an associative array.
Notes about the implementation: